Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

Background

Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154^T provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host–pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model.

Results

We showed that the infection of the host is characterised by an enhancement of functions associated with antibiotic and glucans catabolism functions but a reduction of sulfate assimilation process in T. maritimum. The fish host concurrently displays a large panel of immune effectors, notably involving innate response and triggering acute inflammatory response. In addition, our results suggest that fish activate an adaptive immune response visible through the stimulation of T-helper cells, Th17, with congruent reduction of Th2 and T-regulatory cells. Fish were, however, largely sensitive to infection, and less than 25% survived after 96 hpi. These surviving fish showed no evidence of stress (cortisol levels) or significant difference in microbiome diversity compared with controls at the same sampling time. The presence of T. maritimum in resistant fish skin and the total absence of any skin lesions suggest that these fish did not escape contact with the pathogen, but rather that some mechanisms prevented pathogens entry. In resistant individuals, we detected up-regulation of specific immune-related genes differentiating resistant individuals from controls at 96 hpi, which suggests a possible genomic basis of resistance, although no genetic variation in coding regions was found.

Conclusion

Here we focus in detail on the interplay between common fish pathogens and host immune response during experimental infection. We further highlight key actors of defence response, pathogenicity and possible genomic bases of fish resistance to T. maritimum.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00097-1.

The Mars 2020 Engineering Cameras and Microphone on the Perseverance Rover: A Next-Generation Imaging System for Mars Exploration

The Mars 2020 Perseverance rover is equipped with a next-generation engineering camera imaging system that represents an upgrade over previous Mars rover missions. These upgrades will improve the operational capabilities of the rover with an emphasis on drive planning, robotic arm operation, instrument operations, sample caching activities, and documentation of key events during entry, descent, and landing (EDL). There are a total of 16 cameras in the Perseverance engineering imaging system, including 9 cameras for surface operations and 7 cameras for EDL documentation. There are 3 types of cameras designed for surface operations: Navigation cameras (Navcams, quantity 2), Hazard Avoidance Cameras (Hazcams, quantity 6), and Cachecam (quantity 1). The Navcams will acquire color stereo images of the surface with a 96 ∘ × 73 ∘ field of view at 0.33 mrad/pixel. The Hazcams will acquire color stereo images of the surface with a 136 ∘ × 102 ∘ at 0.46 mrad/pixel. The Cachecam, a new camera type, will acquire images of Martian material inside the sample tubes during caching operations at a spatial scale of 12.5 microns/pixel. There are 5 types of EDL documentation cameras: The Parachute Uplook Cameras (PUCs, quantity 3), the Descent stage Downlook Camera (DDC, quantity 1), the Rover Uplook Camera (RUC, quantity 1), the Rover Descent Camera (RDC, quantity 1), and the Lander Vision System (LVS) Camera (LCAM, quantity 1). The PUCs are mounted on the parachute support structure and will acquire video of the parachute deployment event as part of a system to characterize parachute performance. The DDC is attached to the descent stage and pointed downward, it will characterize vehicle dynamics by capturing video of the rover as it descends from the skycrane. The rover-mounted RUC, attached to the rover and looking upward, will capture similar video of the skycrane from the vantage point of the rover and will also acquire video of the descent stage flyaway event. The RDC, attached to the rover and looking downward, will document plume dynamics by imaging the Martian surface before, during, and after rover touchdown. The LCAM, mounted to the bottom of the rover chassis and pointed downward, will acquire 90 ∘ × 90 ∘ FOV images during the parachute descent phase of EDL as input to an onboard map localization by the Lander Vision System (LVS). The rover also carries a microphone, mounted externally on the rover chassis, to capture acoustic signatures during and after EDL. The Perseverance rover launched from Earth on July 30th, 2020, and touchdown on Mars is scheduled for February 18th, 2021.

Attenuating PI3K isoforms in pancreatic cancer: Focus on immune PI3Kγ

Phosphoinositide 3-kinases PI3Ks are major drug targets in oncology. Their role is far from being completely understood in pancreatic ductal adenocarcinoma. Pancreatic cancer is a dismal disease with limited therapeutic options except for surgery. We highlight here two elegant works demonstrating the role of PI3Kγ in cancer-associated macrophages applied in particular to pancreatic tumors. These data open new avenues for the use of PI3K-targetting drugs in cancer as anti-stroma therapies. Amongst the classI PI3K isoforms, PI3Kγ and PI3Kδ, are highly expressed in immune cells. Isoform-specific or pan-class I PI3K inhibitors which target all classI PI3Ks could be used as a targeted therapy towards cancer cell signaling but also as immunotherapies. Research on immunoregulation of human pancreatic cancer by the other ubiquitous α- or β-isoforms of PI3K needs to be performed.

Use of fluorescent in-situ hybridisation in salivary gland cytology: A powerful diagnostic tool

OBJECTIVE

Salivary gland cytology is challenging because it includes a diversity of lesions and a wide spectra of tumours. Recently, it has been reported that many types of salivary gland tumours have specific molecular diagnostic signatures that could be identified by fluorescent in-situ hybridisation (FISH). The aim of the present study was to demonstrate the feasibility and efficiency of FISH on routine cytological salivary gland smears.

METHODS

FISH was conducted on 37 cytological salivary gland smears from 34 patients. According to the cytological diagnosis suspected, MECT1/MAML2 gene fusion and rearrangements of PLAG1, MYB, or ETV6 were analysed. The presence and percentages of cells that had gene rearrangements were evaluated. Results were compared with the histological surgical samples, available from 26 patients.

RESULTS

The PLAG1 rearrangement was observed in 12/20 (60%) cases of pleomorphic adenoma. MECT1/MAML2 gene fusion was observed in 1:2 mucoepidermoid carcinomas but was not observed in five other tumours (two pleomorphic adenomas, one Warthin's tumour, one mammary analogue secretory carcinoma [MASC] and one cystic tumour). MYB rearrangement was observed in 4/4 adenoid cystic carcinomas. ETV6-gene splitting identified one MASC.

CONCLUSION

Overall, FISH had a specificity of 100% and a sensitivity of 66.7%. When FISH and cytological analyses were combined, the overall sensitivity was increased to 93.3%. It can thus be concluded that when the FISH analysis is positive, the extent of surgery could be determined with confidence pre-operatively without needing a diagnosis from a frozen section.

Immunocytochemical staining for p53 and Ki-67 helps to characterise urothelial cells in urine cytology

OBJECTIVE

The presence of atypical cells in urine cytology is unsatisfactory for both cytologists and clinicians. The objective of this study was to test whether p53 and Ki-67 immunostaining could improve urothelial carcinoma (UC) detection on urinary cytology.

METHODS

A total of 196 urine samples were analysed, 142 from the bladder, 41 from the upper tract and 13 from ileal bladder replacement. Cytology results were expressed as normal (N) (n = 81), atypia cannot exclude low-grade UC (ALG) (n = 25), suspicious for high-grade UC (SHG) (n = 39) and high-grade UC (HG) (n = 51). Actual diagnoses were confirmed by histopathological analysis, cystoscopic examination or follow-up for at least 1 year. Immunocytochemistry performed on CytoSpin^™ slides allowed the determination of the percentage of positive cells with p53 and Ki-67.

RESULTS

The median percentage values [first to third quartile] of p53 and Ki-67 were 0 [0-5] and 0 [0-1] for N cytology, 5 [0-40] and 2 [1-10] for ALG, 10 [0-30] and 6 [3-25] for SHG, and 30 [10-80] and 20 [10-30] for HG, respectively. Statistically higher values were observed for both tests (P < 0.001) in positive cytologies (ALG, SHG and HG). The optimal cut-offs were 5% for p53 and 3% for Ki-67. The sensitivity and specificity for the detection of all UC were 86.4% and 76.7% for cytology alone, 81.3% and 93.2% for cytology and p53, 75.7% and 88% for cytology and Ki-67, and 68.9% and 97.5% for cytology, p53 and Ki-67, respectively.

CONCLUSION

Using p53 and/or Ki-67 in addition to cytology increases the specificity without penalising the sensitivity.

Helicobacter pylori infection: anything new should we know?

Over the past year, 2003-4, there have been a number of studies consolidating previous work in relation to pathogenesis of disease, diagnosis and management of Helicobacter pylori. Studies into the pathogenesis of disease have identified the main adhesin of H. pylori as an important virulence marker and as a potential target for therapy. Molecular investigations of both the strain and host variations have identified the action of several of the virulence factors, e.g. cagA, vacA, on disrupting host cell signalling and the consequences in respect of the release of chemokines from the damaged gastric epithelium and the effect on apoptosis. Over the past year, there have been further diagnostic kits developed based on modifications of current technology. Two promising areas of research for diagnosis are the use of host/strain genome polymorphisms as a means of identifying high-risk patients who may develop severe disease and the use of proteomics to identify potential antigens of diagnostic (or therapeutic) use. The three main antibiotics that are used in first-line eradication regimens are clarithromycin, metronidazole and amoxycillin. Of these, metronidazole has the highest prevalence of resistance, followed by clarithromycin; amoxycillin resistance is only rarely reported. The decreasing success of current first-line therapy is the driving force for the development of new antibiotic combinations and a search for novel sources for chemotherapeutic agents and novel therapeutic targets.

Review article: diagnosis and treatment of Helicobacter: a 2002 updated review

The year 2002 saw advances on many fronts in the study of Helicobacter and gastroduodenal disease. Several studies have confirmed endoscopy as a valuable management procedure with confirmation of the diagnostic utility of the rapid urease test and the description of a new formulation of the test, which is more rapid in giving a result. Serology has been re-confirmed as a useful investigation in selected populations. Some commercial kits for near patient testing have also been assessed and although generally regarded as less accurate than laboratory based tests some have shown acceptable accuracy. The recent exciting development in diagnostic serology is the availability of the faecal antigen test; further studies have confirmed its usefulness as recommended screening tests. There have been several studies demonstrating that a test and treat policy has a significant patient benefit, both economic and medical, although there is some doubt if eradication of Helicobacter leads to regression of atrophy and metaplasia. However, in low Helicobacter-prevalence areas the test and treat policy is being challenged as an effective management strategy. Further studies have shown that compliance with treatment regimens is an important determinant of successful eradication. Finally several new eradication regimens have been reported particularly for use in patients who have had previous unsuccessful eradication attempts.

Review article: Helicobacter pylori infection from pathogenesis to treatment--a critical reappraisal

The main areas of this review are Helicobacter pylori and disease pathogenesis; the relationship of H. pylori to lower gastrointestinal diseases, liver disease and extra-gastrointestinal conditions; the relationship of H. pylori to gastro-oesophageal reflux disease; infection in the very young and very old; diagnostic techniques; and management of H. pylori infections with particular emphasis on eradication regimens and antibiotic resistance.

Reuse of reclaimed wastewater for golf course irrigation in Tunisia

In Tunisia, golf courses are irrigated with secondary treated effluent stored in landscape impoundments. The impact of the conveyance and storage steps on the physical-chemical and biological quality of irrigation water was evaluated on three golf courses over two years. It was found that the water quality varies all along the water route, from the wastewater treatment plant up to the irrigation site: nutrient and bacteria contents decreased along the route in the three cases. This variation depends on the wastewater quality, the length of the pipes conveying water, the number of regulation reservoirs and ponds, the water residence time in pipes, reservoirs and ponds, and the operation of the ponds. The bacteriological quality of irrigation water deteriorates during the irrigation period in the three golf courses as the ponds are operated as continuous flow reactors. The results obtained in this study indicate the inability of golf water supplies, as currently managed, to properly sanitize reclaimed wastewater and meet target quality criteria recommended by WHO (1989) for water intended for recreational use. For a safe reuse of reclaimed wastewater for golf course irrigation, changes in the design and operation of the ponds should be planned or additional treatment steps provided.

Two-dimensional spatial and temporal displacement and deformation field fitting from cardiac magnetic resonance tagging

Tagged magnetic resonance imaging is a specially developed technique to noninvasively assess contractile function of the heart. Several methods have been developed to estimate myocardial deformation from tagged image data. Most of these methods do not explicitly impose a continuity constraint through time although myocardial motion is a continuous physical phenomenon. In this paper, we propose to model the spatio-temporal myocardial displacement field by a cosine series model fitted to the entire tagged dataset. The method has been implemented in two dimensions (2D)+time. Its accuracy was successively evaluated on actual tagged data and on a simulated two-dimensional (2D) moving heart model. The simulations show that an overall theoretical mean accuracy of 0.1 mm can be attained with adequate model orders. The influence of the tagging pattern was evaluated and computing time is provided as a function of the model complexity and data size. This method provides an analytical and hierarchical model of the 2D+time deformation inside the myocardium. It was applied to actual tagged data from a healthy subject and from a patient with ischemia. The results demonstrate the adequacy of the proposed model for this evaluation.

Increased N-linked glycosylation leading to oversialylation of monomeric immunoglobulin A1 from patients with Sjögren's syndrome

Increased serum immunoglobulin A (IgA) level is a common finding in primary Sjögren's syndrome (pSS). IgA might not be properly eliminated because of an abnormal glycosylation. We reported previously that IgA1 from patients with pSS was oversialylated. We extend this finding by showing that monomeric IgA1 contains more sialic acid (SA) in patients than in controls, as determined by enzyme-linked immunosorbent assay (ELISA) and Western blot with Sambucus nigra agglutinin (SNA), a lectin specific for SA. To localize this excess of SA on the N- and/or O-linked oligosaccharides, we analysed them separately, using N- and O-linked oligosaccharide profiling kits based on fluorophore-assisted carbohydrate electrophoresis. N-linked, but not O-linked, oligosaccharides of patients' IgA1 were oversialylated, and this seemed to be linked to an excess of SA on the same number of polysaccharides as normal IgA1. To localize the abnormality to the Fab and/or Fc fragments, monomeric IgA1 was digested with protease, separated and transferred to nitrocellulose, where SA was identified by SNA. Both Fab and Fc fragments appeared to be oversialylated. Oversialylation of N-linked oligosaccharides of IgA1 from patients with pSS might prevent the recognition of IgA by receptors that are responsible for their clearance, resulting in an excess of serum IgA and related immune complexes.

Enhanced sialyltransferase activity in B lymphocytes from patients with primary Sjögren's syndrome

Despite the indisputable role of immunoglobulin (Ig)A in the pathogenesis of primary Sjögren syndrome (pSS), the causative abnormality remains largely unknown. As an extension of our report that IgA is oversialylated in this disease, the thrust of the present study was to measure the sialyltransferase (ST) activity in B lymphocytes. ST containing lysates of B cells from 17 pSS patients and 10 controls, were obtained using a combination of detergents, and incubated with affinity purified IgA that had been previously desialylated. The deposition of cytidine 5' monophosphate sialic acid (SA) by ST from B cells onto IgA was detected by two ELISA based upon the use of biotinylated lectins (Sambucus nigra agglutinin which is specific for alpha2-6 SA and Maackia amurensis which is specific for alpha2-3 SA). In parallel, the amount of SA on IgA from ten of the 17 patients and eight of the 10 controls was assayed using the same method. An excess of alpha2-3 and alpha2-6 SA on IgA was found in those patients with excessive activity of alpha2-3 and alpha2-6 ST. Thus, IgA hypersialylation in pSS patients may result from undue activity of ST.

Image analysis method to assess adhesion of Helicobacter pylori to gastric epithelium using confocal laser scanning microscopy

We have used confocal scanning microscopy of FITC-labelled bacteria to assess binding of Helicobacter pylori to stomach sections and to assess the effect of inhibitors on binding to the Lewis antigens. We have quantified the binding using an image manipulation package that is readily available on the web. Our results demonstrate heterogeneity of binding of Helicobacter pylori to tissue sections and that binding can be inhibited using synthetic Lewis B oligosaccharide.

Glycosylation of immunoglobulin A influences its receptor binding

Immunoglobulin A (IgA), which is heavily glycosylated, interacts with a variety of receptors, e.g. the asialoglycoprotein receptor (ASGP-R), which binds terminal galactose residues, and the Fcalpha receptor (FcalphaRI). It has thus been proposed that elevated serum levels of IgA in primary Sjögren's syndrome (pSS) are caused by its defective clearance. To test this hypothesis, we developed a method (based on sialyl transferases eluted from a hepatoma cell line) to increase the amount of sialic acid (SA) on IgA, and used a battery of IgA1- and IgA2-specific glycosidases to reduce this amount. Binding of IgA1 and IgA2 to ASGP-R and FcalphaRI was found to be sugar dependent because oversialylated IgA bound less than native or desialylated IgA. However, individual sugars did not play a direct role in this binding. Given that IgA are oversialylated in pSS, defective clearance of IgA may indeed be ascribed to an excess of SA in IgA1 and IgA2.

Erythropoietin blood level is increased in sudden infant death

Erythropoietin (EPO) is the main red cell growth factor and its release into the blood stream is stimulated by anemia and also by various kinds of hypoxia. We studied the blood EPO concentration in a population of 96 infants who died suddenly and compared their mean EPO levels to control infants. The normal values were low at birth and progressively increased during the first 2 years. In the sudden infant death (SID) group the EPO level was significantly higher (p = 0.001) for the entire population and particularly in the youngest group (0-2 months): 14.7 +/- 2.4 IU/l (mean +/- SEM) in SID group vs. 3.6 +/- 0.4 IU/l in control group (p < 0.001). Although we could not analyze the blood hemoglobin concentration after death, the anemia hypothesis was refuted by an assay of the percentage of fetal hemoglobin which was normal for age in the control and SID groups. Moreover, there was no significant difference in EPO levels between explained and unexplained deaths. We also observed an increase in the stress hormones, cortisol and beta-endorphin, in the entire SID group. These SID results suggest a profound and long-lasting hypoxia at least during terminal agony.

Changes in glycosylation of immunoglobulins in primary Sjögren's syndrome

Serum IgG and IgA are glycoprotein and significant glycoform abnormalities have been established in primary Sjögren's syndrome. The proportion of asialylated IgG is abnormally high in the patients, whereas IgA1 and IgA2 appear to be over-sialylated. This peculiarity might explain the defective binding of IgA to asialoglycoreceptors. Furthermore, the activity of alpha 2,6 sialyl transferase is higher in the IgA-producing B cells from the patients than in the controls, whereas the alpha 2,3 sialyl transferase operates in the former cells but not in the latter. The mechanism of this enzyme dysregulation warrants elucidation.

Practical usefulness of IgA-containing immune complex determination in the serum of patients with primary Sjögren's syndrome

OBJECTIVE

To evaluate the relevance of IgA-containing immune complexes (IC) as a predictor of lymphocytic infiltration of the minor salivary glands, and thus to determine the necessity of the minor salivary gland biopsy as a diagnostic test for primary Sjögren's syndrome (SS) in patients complaining of dryness of the mouth.

METHODS

IgA-containing IC, as well as anti-SSA and anti-SSB antibodies, were measured using enzyme-linked immunosorbent assays in 116 consecutive patients presenting with dry mouth but no connective tissue disease. The specificity, sensitivity, and positive (PPV) and negative predictive values (NPV) of these tests were calculated in relation to the results of the minor salivary gland biopsy and to the criteria for primary SS.

RESULTS

Sixty-five patients had a focus score > or = 1.IgA-containing IC were detected in 45 of them, compared with five of the remainder (specificity 89%, sensitivity 69%, PPV = 88% and NPV = 69%). When the IgA-containing IC, and the anti-SSA and anti-SSB tests were associated, the sensitivity and NPV were improved (81 and 79%, respectively), while specificity and PPV were maintained (88 and 90%, respectively).

CONCLUSION

Given the reliability of this combination of tests for the diagnosis of primary SS, the minor salivary gland biopsy might be indicated only in those patients without any serological abnormality.

Aberrant glycosylation of IgA from patients with IgA nephropathy

Despite the prominent role of IgA, particularly IgA1, in the pathogenesis of IgA nephropathy (IgAN), the precise role of this molecule in the process remains unclear. Four biotin-conjugated lectins in sandwich-type enzyme-linked immunosorbent assays were devised to determine the glycosylation profiles of total IgA and its subclasses. We took advantage of differential binding properties of these lectins to sugar residues to dissect the oligosaccharide chains O-linked to the hinge and those N-linked to the Fc region of total IgA and IgA subclasses in 47 patients with IgAN and an equal number of controls. The proportion of sialylated IgA1 was higher in patients compared with controls (p < 0.02), whereas IgA2 in patients appeared less well sialylated. A reduction of galactose in pathological IgA as detected by RCA-I became significant after treatment of the molecule with neuraminidase (p < 0.01). Defective galactosylation was also observed for patient IgA1 when it was probed with ECL, a lectin that has a specificity for Gal 1,4 N-acetylglucosamine groupings on N-linked oligosaccharides. The RCA and ECL results, therefore, suggest that increased sialylation on the IgA1 is on O-linked oligosaccharides in the hinge region. This was partly confirmed by a small increase in the binding of PNA to IgA1 from the patient group. This lectin binds preferentially to Gal 1,3 N-acetylgalactosamine groups that are found on O-linked oligosaccharides.